data_6O9V # _model_server_result.job_id W6ok4dAmByutk67zqos17A _model_server_result.datetime_utc '2025-02-28 20:51:06' _model_server_result.server_version 0.9.12 _model_server_result.query_name ligand _model_server_result.source_id pdb-bcif _model_server_result.entry_id 6o9v # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"J","auth_seq_id":403}' # _entry.id 6O9V # _exptl.entry_id 6O9V _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 75.11 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'trimethylamine oxide' _entity.pdbx_number_of_molecules 2 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 90 _cell.angle_gamma 90 _cell.entry_id 6O9V _cell.length_a 83.298 _cell.length_b 114.683 _cell.length_c 89.457 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6O9V _symmetry.cell_setting ? _symmetry.Int_Tables_number 18 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I,J,K,L,M _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 2_455 -x-1,-y,z -1 0 0 0 -1 0 0 0 1 -83.298 0 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 C N N ? 2 J N N # loop_ _struct_conn.conn_type_id _struct_conn.details _struct_conn.id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_PDB_id _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order covale ? covale1 A SG CYS 129 A CYS 129 1_555 H S01 M1M . B M1M 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.084 ? covale ? covale2 A SG CYS 135 A CYS 135 1_555 I S03 M1M . B M1M 402 2_455 ? ? ? ? ? ? ? ? ? ? ? ? 2.083 ? covale ? covale3 B SG CYS 129 B CYS 129 1_555 I S01 M1M . B M1M 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.085 ? covale ? covale4 B SG CYS 135 B CYS 135 1_555 H S03 M1M . B M1M 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.079 ? metalc ? metalc1 A O THR 96 A THR 96 1_555 E K K . A K 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.19 ? metalc ? metalc2 A O THR 96 A THR 96 1_555 E K K . A K 403 2_455 ? ? ? ? ? ? ? ? ? ? ? ? 3.19 ? metalc ? metalc3 A O THR 96 A THR 96 1_555 F K K . A K 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.753 ? metalc ? metalc4 A OG1 THR 96 A THR 96 1_555 F K K . A K 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.04 ? metalc ? metalc5 A O THR 96 A THR 96 1_555 F K K . A K 404 2_455 ? ? ? ? ? ? ? ? ? ? ? ? 2.753 ? metalc ? metalc6 A OG1 THR 96 A THR 96 1_555 F K K . A K 404 2_455 ? ? ? ? ? ? ? ? ? ? ? ? 3.04 ? metalc ? metalc7 A O ILE 97 A ILE 97 1_555 E K K . A K 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.765 ? metalc ? metalc8 A O ILE 97 A ILE 97 1_555 E K K . A K 403 2_455 ? ? ? ? ? ? ? ? ? ? ? ? 2.765 ? metalc ? metalc9 A O GLY 98 A GLY 98 1_555 D K K . A K 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.765 ? metalc ? metalc10 A O GLY 98 A GLY 98 1_555 D K K . A K 402 2_455 ? ? ? ? ? ? ? ? ? ? ? ? 2.765 ? metalc ? metalc11 A O TYR 99 A TYR 99 1_555 D K K . A K 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.856 ? metalc ? metalc12 A O TYR 99 A TYR 99 1_555 D K K . A K 402 2_455 ? ? ? ? ? ? ? ? ? ? ? ? 2.856 ? metalc ? metalc13 D K K . A K 402 1_555 B O GLY 98 B GLY 98 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.834 ? metalc ? metalc14 D K K . A K 402 2_455 B O GLY 98 B GLY 98 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.834 ? metalc ? metalc15 D K K . A K 402 1_555 B O TYR 99 B TYR 99 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.787 ? metalc ? metalc16 D K K . A K 402 2_455 B O TYR 99 B TYR 99 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.787 ? metalc ? metalc17 E K K . A K 403 1_555 B O THR 96 B THR 96 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.805 ? metalc ? metalc18 E K K . A K 403 2_455 B O THR 96 B THR 96 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.805 ? metalc ? metalc19 E K K . A K 403 1_555 B O ILE 97 B ILE 97 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.813 ? metalc ? metalc20 E K K . A K 403 2_455 B O ILE 97 B ILE 97 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.813 ? metalc ? metalc21 F K K . A K 404 1_555 B O THR 96 B THR 96 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.911 ? metalc ? metalc22 F K K . A K 404 1_555 B OG1 THR 96 B THR 96 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.793 ? metalc ? metalc23 F K K . A K 404 2_455 B O THR 96 B THR 96 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.911 ? metalc ? metalc24 F K K . A K 404 2_455 B OG1 THR 96 B THR 96 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.793 ? # _chem_comp.formula 'C3 H9 N O' _chem_comp.formula_weight 75.11 _chem_comp.id TMO _chem_comp.mon_nstd_flag . _chem_comp.name 'trimethylamine oxide' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # loop_ _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.comp_id _chem_comp_bond.value_order _chem_comp_bond.pdbx_ordinal _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_aromatic_flag CAA NAC TMO sing 364 n n CAA HAA TMO sing 365 n n CAA HAAA TMO sing 366 n n CAA HAAB TMO sing 367 n n NAC CAD TMO sing 368 n n NAC CAB TMO sing 369 n n NAC OAE TMO sing 370 n n CAD HAD TMO sing 371 n n CAD HADA TMO sing 372 n n CAD HADB TMO sing 373 n n CAB HAB TMO sing 374 n n CAB HABA TMO sing 375 n n CAB HABB TMO sing 376 n n # _atom_sites.entry_id 6O9V _atom_sites.fract_transf_matrix[1][1] 0.012005 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.00872 _atom_sites.fract_transf_matrix[2][3] 0 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.011179 _atom_sites.fract_transf_vector[1] 0 _atom_sites.fract_transf_vector[2] 0 _atom_sites.fract_transf_vector[3] 0 # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_ins_code C 2 TMO A 1 401 1 TMO TMO . D 3 K A 1 402 1 K K . E 3 K A 1 403 3 K K . F 3 K A 1 404 4 K K . G 4 DDQ A 1 405 1 DDQ LD3 . H 5 M1M B 1 401 500 M1M MTS . I 5 M1M B 1 402 500 M1M MTS . J 2 TMO B 1 403 2 TMO TMO . K 4 DDQ B 1 404 2 DDQ LD3 . L 6 HOH A 1 501 20 HOH HOH . L 6 HOH A 2 502 17 HOH HOH . L 6 HOH A 3 503 12 HOH HOH . L 6 HOH A 4 504 10 HOH HOH . L 6 HOH A 5 505 6 HOH HOH . L 6 HOH A 6 506 25 HOH HOH . L 6 HOH A 7 507 22 HOH HOH . L 6 HOH A 8 508 13 HOH HOH . L 6 HOH A 9 509 21 HOH HOH . M 6 HOH B 1 501 9 HOH HOH . M 6 HOH B 2 502 7 HOH HOH . M 6 HOH B 3 503 24 HOH HOH . M 6 HOH B 4 504 15 HOH HOH . M 6 HOH B 5 505 28 HOH HOH . M 6 HOH B 6 506 16 HOH HOH . M 6 HOH B 7 507 23 HOH HOH . M 6 HOH B 8 508 4 HOH HOH . M 6 HOH B 9 509 18 HOH HOH . M 6 HOH B 10 510 3 HOH HOH . M 6 HOH B 11 511 26 HOH HOH . M 6 HOH B 12 512 5 HOH HOH . # loop_ _atom_site.group_PDB _atom_site.id _atom_site.type_symbol _atom_site.label_atom_id _atom_site.label_comp_id _atom_site.label_seq_id _atom_site.label_alt_id _atom_site.pdbx_PDB_ins_code _atom_site.label_asym_id _atom_site.label_entity_id _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _atom_site.occupancy _atom_site.B_iso_or_equiv _atom_site.pdbx_formal_charge _atom_site.auth_atom_id _atom_site.auth_comp_id _atom_site.auth_seq_id _atom_site.auth_asym_id _atom_site.pdbx_PDB_model_num HETATM 1 C CAA TMO . . . J 2 -38.638 2.019 -33.588 0.62 60.8 ? CAA TMO 403 B 1 HETATM 2 N NAC TMO . . . J 2 -37.656 1.09 -34.117 0.62 75.98 1 NAC TMO 403 B 1 HETATM 3 C CAD TMO . . . J 2 -38.14 -0.268 -33.947 0.62 62.78 ? CAD TMO 403 B 1 HETATM 4 C CAB TMO . . . J 2 -37.445 1.358 -35.528 0.62 91.92 ? CAB TMO 403 B 1 HETATM 5 O OAE TMO . . . J 2 -36.443 1.247 -33.431 0.62 69.4 -1 OAE TMO 403 B 1 # _model_server_stats.io_time_ms 69 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 311 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 5 #